Q: There's a huge difference between my peak number and the bio company's peak number

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MACS -- Model-based Analysis of ChIP-Seq

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Q: There's a huge difference between my peak number and the bio company's peak number #673

Open bigshark12345 opened 1 week ago

bigshark12345 commented 1 week ago

When I use macs3 call peak(for atac), I only get 5500 peaks, But when I checked the bio company's report, they got a peak of 30,000. I want to know the possible reasons。 Here's my code： macs3 callpeak -g 762311306 -t MF-1-A.final.bam --name ./MF1A -B --format BAM --qvalue 0.075 --cutoff-analysis --broad --nomodel --shift -75 --extsize 150

taoliu commented 1 week ago

@bigshark12345 Did the bio company use the same parameters as those in your command? By the way, I would suggest you not using --broad for ATAC-seq data analysis. The peaks in ATAC-seq is not supposed to be 'broad' as some histone marks for which the 'broad mode' was designed for.